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Mutant Information

Mutant Name	FN1475-S [Download]
Generation	M2
Genus Species	Oryza Sativa
Cultivar	Kitaake
Alignment File (BAM File)	Download FN1475-S Alignment File
Seed Availability	Yes [Order Seeds]
Phenotype	TO:0000326 (Leaf Color) = Normal TO:0000137 (Days to heading) = Normal (Between 75% and 125%) TO:0000346 (Tiller number) = Normal (Between 75% and 125%) TO:0000430 (Germination Rate) = Normal (Between 75% and 125%) For more information, please see this phenotype file

Variant Information

Single base substitutions: 37

Variant Type

Chromosome

Position

Change

Genotype

Effect

Gene Affected

SBS Chr1 12412003 G-A Hetero INTERGENIC
SBS Chr1 14443219 T-C Hetero INTERGENIC
SBS Chr1 31821556 A-T Homo INTRON
SBS Chr1 31839138 T-G Homo INTERGENIC
SBS Chr1 39919338 C-T Hetero INTERGENIC
SBS Chr2 5617886 A-C Hetero INTRON
SBS Chr2 30847670 G-A Homo INTERGENIC
SBS Chr3 14678221 C-A Hetero INTERGENIC
SBS Chr3 16809315 C-A Hetero INTERGENIC
SBS Chr3 17632470 C-T Hetero INTERGENIC
SBS Chr3 20828485 C-T Hetero INTERGENIC
SBS Chr3 21936735 C-T Homo INTERGENIC
SBS Chr3 30285363 C-T Hetero NON_SYNONYMOUS_CODING OsKitaake03g317800
SBS Chr4 20916773 C-T Homo INTERGENIC
SBS Chr5 762701 G-T Homo INTERGENIC
SBS Chr5 5939374 T-A Hetero INTERGENIC
SBS Chr5 12765650 G-A Hetero INTERGENIC
SBS Chr5 18951399 A-T Hetero INTERGENIC
SBS Chr5 24427587 A-G Hetero NON_SYNONYMOUS_CODING OsKitaake05g197700
SBS Chr6 24830759 T-A Hetero NON_SYNONYMOUS_CODING OsKitaake06g220700
SBS Chr7 2456734 A-C Hetero INTRON
SBS Chr7 5006594 A-G Hetero INTERGENIC
SBS Chr7 10752371 C-T Hetero INTERGENIC
SBS Chr7 11227311 T-C Hetero INTERGENIC
SBS Chr7 12370954 G-A Hetero INTERGENIC
SBS Chr7 26206002 C-T Hetero INTRON
SBS Chr8 20044297 A-T Hetero NON_SYNONYMOUS_CODING OsKitaake08g147500
SBS Chr9 6685129 T-A Homo INTERGENIC
SBS Chr9 11033331 C-T Hetero INTERGENIC
SBS Chr9 12163197 G-A Hetero INTERGENIC
SBS Chr9 13076648 G-A Hetero INTERGENIC
SBS Chr9 14521399 C-A Hetero INTERGENIC
SBS Chr9 17636176 A-T Homo INTERGENIC
SBS Chr9 17636177 C-G Homo INTERGENIC
SBS Chr10 21426763 G-A Hetero INTERGENIC
SBS Chr12 7917297 G-A Hetero INTERGENIC
SBS Chr12 9005132 T-C Hetero INTERGENIC

Deletions: 40

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Deletion Chr7 1 18000 17999
Deletion Chr1 368001 380000 11999 OsKitaake01g005200
Deletion Chr5 571001 584000 12999 2
Deletion Chr6 746001 772000 25999 2
Deletion Chr2 931001 940000 8999 OsKitaake02g013300
Deletion Chr2 1638001 1652000 13999 OsKitaake02g025800
Deletion Chr1 1861001 1871000 9999 2
Deletion Chr3 2527001 2538000 10999 OsKitaake03g035600
Deletion Chr3 4418001 4434000 15999
Deletion Chr2 6213001 6233000 19999 3
Deletion Chr1 9647001 9660000 12999 OsKitaake01g123400
Deletion Chr10 12484001 12495000 10999 2
Deletion Chr8 12535001 12544000 8999 OsKitaake08g107500
Deletion Chr1 13461001 13472000 10999 OsKitaake01g156600
Deletion Chr2 16077001 16100000 22999 OsKitaake02g166300
Deletion Chr3 16709001 16718000 8999 OsKitaake03g210400
Deletion Chr4 16969706 16969714 8
Deletion Chr10 17478001 17492000 13999 OsKitaake10g119300
Deletion Chr10 19376001 19385000 8999 OsKitaake10g141100
Deletion Chr2 20775001 20783000 7999 OsKitaake02g201300
Deletion Chr8 21298001 21309000 10999 OsKitaake08g159900
Deletion Chr9 21533156 21533169 13
Deletion Chr3 22414807 22414808 1
Deletion Chr1 22725741 22725742 1
Deletion Chr4 22739001 22756000 16999 6
Deletion Chr7 22895001 22921000 25999 2
Deletion Chr12 23743001 23750000 6999 OsKitaake12g191000
Deletion Chr7 24380001 24394000 13999 OsKitaake07g217100
Deletion Chr4 24461001 24474000 12999
Deletion Chr6 25966001 25974000 7999 OsKitaake06g231700
Deletion Chr1 26060001 26069000 8999
Deletion Chr4 26729001 26738000 8999 OsKitaake04g193100
Deletion Chr6 26994966 26994967 1
Deletion Chr12 27143001 27154000 10999
Deletion Chr7 27678001 27688000 9999 OsKitaake07g258500
Deletion Chr7 28264105 28264109 4
Deletion Chr1 33452001 33473000 20999 OsKitaake01g342500
Deletion Chr2 33696001 33707000 10999 OsKitaake02g348500
Deletion Chr3 37707001 37715000 7999 OsKitaake03g423700
Deletion Chr1 41005001 41014000 8999 OsKitaake01g447600

Insertions: 3

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Insertion Chr7 3837732 3837735 2
Insertion Chr10 3988865 3988869 3
Insertion Chr5 30239995 30240003 7

Inversions: 3

Variant Type

Chromosome

Position 1

Position 2

Number of Genes

Inversion Chr1 5302726 5401393 OsKitaake01g069900
Inversion Chr1 5303790 5401405 OsKitaake01g069900
Inversion Chr8 19532843 20015770

Translocations: 1

Variant Type

Chromosome

Position 1

Chromosome

Position 2

Number of Genes

Translocation Chr8 19532835 Chr1 5303766

Variant Type	Chromosome	Position	Change	Genotype	Effect	Gene Affected
SBS	Chr1	12412003	G-A	Hetero	INTERGENIC
SBS	Chr1	14443219	T-C	Hetero	INTERGENIC
SBS	Chr1	31821556	A-T	Homo	INTRON
SBS	Chr1	31839138	T-G	Homo	INTERGENIC
SBS	Chr1	39919338	C-T	Hetero	INTERGENIC
SBS	Chr2	5617886	A-C	Hetero	INTRON
SBS	Chr2	30847670	G-A	Homo	INTERGENIC
SBS	Chr3	14678221	C-A	Hetero	INTERGENIC
SBS	Chr3	16809315	C-A	Hetero	INTERGENIC
SBS	Chr3	17632470	C-T	Hetero	INTERGENIC
SBS	Chr3	20828485	C-T	Hetero	INTERGENIC
SBS	Chr3	21936735	C-T	Homo	INTERGENIC
SBS	Chr3	30285363	C-T	Hetero	NON_SYNONYMOUS_CODING	OsKitaake03g317800
SBS	Chr4	20916773	C-T	Homo	INTERGENIC
SBS	Chr5	762701	G-T	Homo	INTERGENIC
SBS	Chr5	5939374	T-A	Hetero	INTERGENIC
SBS	Chr5	12765650	G-A	Hetero	INTERGENIC
SBS	Chr5	18951399	A-T	Hetero	INTERGENIC
SBS	Chr5	24427587	A-G	Hetero	NON_SYNONYMOUS_CODING	OsKitaake05g197700
SBS	Chr6	24830759	T-A	Hetero	NON_SYNONYMOUS_CODING	OsKitaake06g220700
SBS	Chr7	2456734	A-C	Hetero	INTRON
SBS	Chr7	5006594	A-G	Hetero	INTERGENIC
SBS	Chr7	10752371	C-T	Hetero	INTERGENIC
SBS	Chr7	11227311	T-C	Hetero	INTERGENIC
SBS	Chr7	12370954	G-A	Hetero	INTERGENIC
SBS	Chr7	26206002	C-T	Hetero	INTRON
SBS	Chr8	20044297	A-T	Hetero	NON_SYNONYMOUS_CODING	OsKitaake08g147500
SBS	Chr9	6685129	T-A	Homo	INTERGENIC
SBS	Chr9	11033331	C-T	Hetero	INTERGENIC
SBS	Chr9	12163197	G-A	Hetero	INTERGENIC
SBS	Chr9	13076648	G-A	Hetero	INTERGENIC
SBS	Chr9	14521399	C-A	Hetero	INTERGENIC
SBS	Chr9	17636176	A-T	Homo	INTERGENIC
SBS	Chr9	17636177	C-G	Homo	INTERGENIC
SBS	Chr10	21426763	G-A	Hetero	INTERGENIC
SBS	Chr12	7917297	G-A	Hetero	INTERGENIC
SBS	Chr12	9005132	T-C	Hetero	INTERGENIC

Variant Type	Chromosome	Start	End	Size(bp)	Number of Genes
Deletion	Chr7	1	18000	17999
Deletion	Chr1	368001	380000	11999	OsKitaake01g005200
Deletion	Chr5	571001	584000	12999	2
Deletion	Chr6	746001	772000	25999	2
Deletion	Chr2	931001	940000	8999	OsKitaake02g013300
Deletion	Chr2	1638001	1652000	13999	OsKitaake02g025800
Deletion	Chr1	1861001	1871000	9999	2
Deletion	Chr3	2527001	2538000	10999	OsKitaake03g035600
Deletion	Chr3	4418001	4434000	15999
Deletion	Chr2	6213001	6233000	19999	3
Deletion	Chr1	9647001	9660000	12999	OsKitaake01g123400
Deletion	Chr10	12484001	12495000	10999	2
Deletion	Chr8	12535001	12544000	8999	OsKitaake08g107500
Deletion	Chr1	13461001	13472000	10999	OsKitaake01g156600
Deletion	Chr2	16077001	16100000	22999	OsKitaake02g166300
Deletion	Chr3	16709001	16718000	8999	OsKitaake03g210400
Deletion	Chr4	16969706	16969714	8
Deletion	Chr10	17478001	17492000	13999	OsKitaake10g119300
Deletion	Chr10	19376001	19385000	8999	OsKitaake10g141100
Deletion	Chr2	20775001	20783000	7999	OsKitaake02g201300
Deletion	Chr8	21298001	21309000	10999	OsKitaake08g159900
Deletion	Chr9	21533156	21533169	13
Deletion	Chr3	22414807	22414808	1
Deletion	Chr1	22725741	22725742	1
Deletion	Chr4	22739001	22756000	16999	6
Deletion	Chr7	22895001	22921000	25999	2
Deletion	Chr12	23743001	23750000	6999	OsKitaake12g191000
Deletion	Chr7	24380001	24394000	13999	OsKitaake07g217100
Deletion	Chr4	24461001	24474000	12999
Deletion	Chr6	25966001	25974000	7999	OsKitaake06g231700
Deletion	Chr1	26060001	26069000	8999
Deletion	Chr4	26729001	26738000	8999	OsKitaake04g193100
Deletion	Chr6	26994966	26994967	1
Deletion	Chr12	27143001	27154000	10999
Deletion	Chr7	27678001	27688000	9999	OsKitaake07g258500
Deletion	Chr7	28264105	28264109	4
Deletion	Chr1	33452001	33473000	20999	OsKitaake01g342500
Deletion	Chr2	33696001	33707000	10999	OsKitaake02g348500
Deletion	Chr3	37707001	37715000	7999	OsKitaake03g423700
Deletion	Chr1	41005001	41014000	8999	OsKitaake01g447600

Variant Type	Chromosome	Position 1	Position 2	Number of Genes
Inversion	Chr1	5302726	5401393	OsKitaake01g069900
Inversion	Chr1	5303790	5401405	OsKitaake01g069900
Inversion	Chr8	19532843	20015770

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Variant Type

Chromosome

Position

Change

Genotype

Effect

Gene Affected

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Variant Type

Chromosome

Position 1

Position 2

Number of Genes

Variant Type

Chromosome

Position 1

Chromosome

Position 2

Number of Genes